Panels are part of the AWT and are heavyweight components, meaning that they are closely tied to the underlying OS peer that actually communicates with the hardware. JMenuBars are Swing and are lightweight, so they are not as closely tied to the peer. Mixing the two can cause problems - as you have noticed, the heavyweight ones will stomp on the lightweight ones. Try using a JPanel instead.
"JavaRanch, where the deer and the Certified play" - David O'Meara